As a citizen of a European Union (EU) country who generally tours within europe crossing borders hasn't been a problem.
Living on an island means I have to fly or take a ferry when going abroad and I'm fascinated how everyone talks about boxing or bagging their bike. I've flown Dublin to France numerous times (allways Aer Lingus) and once to Sicily (Ryan Air) and never boxed or bagged my bike. It has always arrived in perfect condition and been ready to roll in about 15 minutes.
The only time I ever boxed my bike was on a trip to Cuba and then only because I had to fly via London, Gatwick and had to change planes.
That time it also arrived safely but I unfortunately I had it stolen on my first day in downtown Havana.